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Actually, when paused, either a separate share or the whole Sync app, files are still indexed. Pausing only stops download.

You might want to disable system notifications and increase rescan interval in power user settings. So Sync will not be notified about whatever files are changed and will rescan the share only at defined intervals (you may put a few hours, for example). This affects all shares in Sync. To force rescan when you need it, restart Sync.

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I don't know if could have sense to disable indexing if folder is in pause, i.e if i put in pause a folder it did not need any indexing from my point of view, it will be indexed when the folder will be not in pause .